Tracking CVS commits

BioPython commits CVS Log

Bio/LogisticRegression.py

Don't use 'from XXXy import *' but instead 'import XXX' (Bug 2676). Fix from Bruce Southey.

Bio/kNN.py

Don't using 'from numpy import *' but instead 'import numppy' (Bug 2675). Fix from Bruce Southey.

Tests/test_kNN.py

Tweaking the numpy import (Bug 2674)

Bio/triemodule.c

More changes for Python 2.5. See bug #2609.

Doc/Tutorial.tex

A few small changes. Added a short section on RPS-BLAST.

Tests/test_docstrings.py

Silently skip doctests for modules needing numpy if numpy isn't installed (Bug 2672)

Tests/test_lowess.py

Skip test if missing numpy (Bug 2672, see also Bug 2534)

Tests/test_GASelection.py

Fixing an occasional unit test failure reported on the mailing list by Bruce Southey: Commenting out the assertion in DiversitySelectionTest.t_no_retrive_organism, since a 100% random new genome could by chance already be in the population.

Tests/test_GASelection.py

Fix for occasional infinite loop when creating the input population in TournamentSelectionTest.t_select_best(); see mailing list discussion.

Tests/test_GAQueens.py

Since Biopython 1.45, or to be exact Bio/Seq.py CVS revision 1.20 (see Bug 2386), the Seq object's count method will not accept an integer argument. Fixes Bug 2651.

Tests/: test_PDB.py, output/test_PDB

Coverted tabs to spaces in test_PDB.py and added a simple test of Bio.PDB.NeighborSearch based on that module's self test.

Bio/KDTree/: KDTree.c, KDTree.h, KDTreemodule.c

Distinguish between memory errors and not finding any entries. See bug #2666.

Bio/PDB/NeighborSearch.py

Self test was re-using the variable i (see also Bug 2666)

Bio/Statistics/lowess.py

See bug #2657; making this code faster.

Tests/: test_lowess.py, output/test_lowess

Adding a test case for Bio.Statistics.lowess; see bug #2657.

Bio/triemodule.c

Updating for Python 2.5. See bug #2609.

Bio/KDTree/KDTree.c

Make the compiler shut up.

Bio/PDB/NeighborSearch.py

This assertion is no longer needed (see revision 1.13 of Bio/KDTree/KDTree.py and revision 1.3 of Bio/KDTree/KDTreemodule.c, and bug #2649), and the typecode method no longer exists in NumPy. See bug #2658.

Doc/Tutorial.tex

Fixed a typo (Bug 2659) and rephrased some of the overview

DEPRECATED

Removing Bio.Ais which was deprecated in Biopython 1.45

Tests/: test_Cluster.py, test_KDTree.py, test_LogisticRegression.py, test_MarkovModel.py, test_PDB.py, test_SVDSuperimposer.py, test_kNN.py

Skip tests which require numpy gracefully (see also Bug 2524)

Tests/test_PopGen_SimCoal.py

Filename case fix for Windows

Bio/SeqRecord.py

Adding a general example doctest to the main docstring for the SeqRecord class (see Bug 2640)

Bio/PopGen/SimCoal/Template.py

Fixing a newline issue under windows (Bug 2638)

Bio/PopGen/SimCoal/Controller.py

Fixed command line redirection on Windows

Bio/PopGen/SimCoal/Controller.py

Fixed case problems with finding SIMCOAL2.EXE under Windows (but unit test still fails for me on Windows)

Bio/Statistics/lowess.py

Adding a simple doctest for Bio.Statistics.lowess (see also Bug 2657)

Bio/Statistics/lowess.py

Switching indentation to standard four spaces. Added missing copyright and license text.

Tests/test_BioSQL_SeqIO.py

Removing two redundant comment lines (see Bug 2655)

BioSQL/BioSeq.py

Feature and sub-features should be sorted in the database by their rank, don't try and resort them. This also resolves the related TODO item in the unit test (Fix from Cymon Cox, see Bug 2655).

BioSQL/BioSeq.py

Patch from Cymon Cox to Include explicit ordering by rank for qualifiers and dbxrefs, fixing the cor6_6.gb unit test example. I'm also recording the SeqFeature primary key as a private property.